Peptidoglycan biosynthetic mura protein from Streptococcus pneumoniae

ABSTRACT

The invention provides isolated nucleic acid compounds encoding the stem peptide biosynthetic gene murA of Streptococcus pneumoniae. Also provided are vectors and transformed heterologous host cells for expressing the MurA enzyme product and a method for identifying compounds that inhibit stem peptide biosynthesis.

BACKGROUND OF THE INVENTION

This invention relates to recombinant DNA technology. In particular the invention pertains to the cloning of the murA gene encoding UDPGlcNAc enolpyruvyl transferase of Streptococcus pneumoniae and the use of the murA gene and the encoded protein in a screen for new inhibitors of bacterial cell wall biosynthesis.

The emergence of antibiotic resistance in common pathogenic bacterial species has justifiably alarmed the medical and research communities. Frequently these organisms are co-resistant to several different antibacterial agents. Pathogens resistant to frequently utilized antibiotics are found in the clinical as well as the community setting. Particularly problematic in the community setting has been the emergence and rapid spread of beta-lactam resistance in Streptococcus pneumoniae which frequently causes upper respiratory tract infections. Resistance to beta-lactams in this organism is due to modification of one or more of the penicillin-binding proteins (PBP's) which are involved in cell wall biosynthesis and are the targets for beta-lactam antibiotics.

Interference with bacterial cell wall biosynthesis is an especially attractive antibacterial target because an analogous structure does not exist in mammalian cells so that compounds that interfere with cell wall biosynthesis have low toxicity in humans and potentially high therapeutic value.

The bacterial cell wall structure contains a peptidoglycan layer which provides mechanical rigidity for the bacterium. This segment of the cell wall is composed of a sugar backbone (alternating residues of N-acetylglucosamine and N-acetylmuramic acid) attached to a pentapeptide (also referred to as "stem peptide," or "Park nucleotide") containing alternating D and L amino acid residues. The nascent peptidoglycan layer is stabilized by an enzymatic step which crosslinks adjacent pentapeptide moieties. Without this crosslinking step the peptidoglycan structure is severely weakened and susceptible to degradation. Indeed, it is the peptidoglycan crosslinking step that has been a frequently targeted site for antibiotic compounds such as the beta-lactam antibiotics.

Unlike the widely targeted peptidoglycan crosslinking step, the stem peptide pathway has not been widely exploited as a target for inhibitory compounds. The stem peptide biosynthetic pathway comprises at least 10 steps in which the stem peptide is added onto UDPMurNAc by the stepwise addition of amino acid residues. In the first step, catalyzed by the UDPGlcNAc enolpyruvyl transferase and NADH-dependent reductase, UDPGlcNAc is converted to UDPMurNAc. In five subsequent steps, catalyzed by UDP-N-acetylmuramate:L-alanine ligase; UDP-N-acetyl-muramyl-L-alanine:D-glutamate ligase; UDP-N-acetyl-muramyl-L-alanyl-D-isoglutamate:L-lysine ligase; UDP-N-acetylmuramyl-L-alanyl-D-isoglutamyl-L-lysine:D-alanyl-D-alanine ligase; and D-alanyl-D-alanine ligase, the final product, UDPMurNAc-L-Ala-D-isoGlu-L-lysine-D-Ala-D-Ala, is produced in Streptococcus pneumoniae.

The enzymatic steps involved in the formation of the stem peptide are potential targets for new antibacterial agents. A few inhibitors, which target this pathway, have been developed. For example, D-cycloserine inhibits alanine racemase and D-alanine-D-alanine ligase; phosphonomycin inhibits the conversion of UDP-GlcNAc to UDP-GlcNac-enolpyruvate; and Ala-phosphonine inhibits the formation of UDP-MurNac-L-Ala.

While inroads in the development of new antibiotics and new targets for antibiotic compounds have emerged in a variety of microorganisms, progress has been less apparent in Streptococcus pneumoniae. In part, Streptococcus pneumoniae presents a special case because this organism is highly mutagenic and readily takes up exogenous DNA from its surroundings. Thus, the need for new antibacterial compounds and new targets for antibacterial therapy is especially acute in Streptococcus pneumoniae.

SUMMARY OF THE INVENTION

The present invention is designed to meet the aforementioned need and provides, inter alia, isolated nucleic acid molecules that encode the murA gene product from Streptococcus pneumoniae. The invention also provides the protein product of the Streptococcus pneumoniae murA gene, UDPGlcNAc enolpyruvyl transferase (MurA protein), in substantially purified form.

Having the cloned murA gene of Streptococcus pneumoniae enables the production of recombinant MurA protein and the implementation of large scale screens to identify new inhibitory compounds targeted at the stem peptide biosynthetic pathway. It may be possible to combine stem peptide proteins in a single screen to examine several steps at the same time. Structural analysis of the MurA protein will enable structure-based drug design to develop novel compounds effective in the treatment of antibiotic resistant microorganisms.

In one embodiment the present invention relates to an isolated DNA molecule encoding MurA protein, said DNA molecule comprising the nucleotide sequence identified as SEQ ID NO. 1:

    __________________________________________________________________________     ATGAAATCAA                                                                             GAGTAAAGGA                                                                             AACGAGTATG                                                                             GATAAAATTG                                                                             TGGTTCAAGG                                                                             TGGCGATAAT                                                                             60                             CGTCTGGTAG                                                                             GAAGCGTGAC                                                                             GATCGAGGGA                                                                             GCAAAAAATG                                                                             CAGTCTTACC                                                                             CTTGTTGGCA                                                                             120                            GCGACTATTC                                                                             TAGCAAGTGA                                                                             AGGAAAGACC                                                                             GTCTTGCAGA                                                                             ATGTTCCGAT                                                                             TTTGTCGGAT                                                                             180                            GTCTTTATTA                                                                             TGAATCAGGT                                                                             AGTTGGTGGT                                                                             TTGAATGCCA                                                                             AGGTTGACTT                                                                             TGATGAGGAA                                                                             240                            GCTCATCTTG                                                                             TCAAGGTGGA                                                                             TGCTACTGGC                                                                             GACATCACTG                                                                             AGGAAGCCCC                                                                             TTACAAGTAT                                                                             300                            GTCAGCAAGA                                                                             TGCGCGCCTC                                                                             CATCGTTGTA                                                                             TTAGGGCCAA                                                                             TCCTTGCCCG                                                                             TGTGGGTCAT                                                                             360                            GCCAAGGTAT                                                                             CCATGCCAGG                                                                             TGGTTGTACG                                                                             ATTGGTAGCC                                                                             GTCCTATTGA                                                                             TCTTCATTTG                                                                             420                            AAAGGTCTGG                                                                             AAGCTATGGG                                                                             GGTTAAGATT                                                                             AGTCAGACAG                                                                             CTGGTTACAT                                                                             CGAAGCCAAG                                                                             480                            GCAGAACGCT                                                                             TGCATGGCGC                                                                             TCATATCTAT                                                                             ATGGACTTTC                                                                             CAAGTGTTGG                                                                             TGCAACGCAG                                                                             540                            AACTTGATGA                                                                             TGGCAGCGAC                                                                             TCTGGCTGAT                                                                             GGGGTGACAG                                                                             TGATTGAGAA                                                                             TGCTGCGCGT                                                                             600                            GAGCCTGAGA                                                                             TTGTTGACTT                                                                             AGCCATTCTC                                                                             CTTAATGAAA                                                                             TGGGAGCCAA                                                                             GGTCAAAGGT                                                                             660                            GCTGGTACAG                                                                             AGACTATAAC                                                                             CATTACTGGT                                                                             GTTGAGAAAC                                                                             TTCATGGTAC                                                                             GACTCACAAT                                                                             720                            GTAGTCCAAG                                                                             ACCGTATCGA                                                                             AGCAGGAACC                                                                             TTTATGGTAG                                                                             CTGCTGCCAT                                                                             GACTGGTGGT                                                                             780                            GATGTCTTGA                                                                             TTCGAGACGC                                                                             TGTCTGGGAG                                                                             CACAACCGTC                                                                             CCTTGATTGC                                                                             CAAGTTACTT                                                                             840                            GAAATGGGTG                                                                             TTGAAGTAAT                                                                             TGAAGAAGAC                                                                             GAAGGAATTC                                                                             GTGTTCGTTC                                                                             TCAACTAGAA                                                                             900                            AATCTAAAAG                                                                             CTGTTCATGT                                                                             GAAAACCTTG                                                                             CCCCACCCAG                                                                             GATTTCCAAC                                                                             AGATATGCAG                                                                             960                            GCTCAATTTA                                                                             CAGCCTTGAT                                                                             GACAGTTGCA                                                                             AAAGGCGAAT                                                                             CAACCATGGT                                                                             GGAGACAGTT                                                                             1020                           TTCGAAAATC                                                                             GTTTCCAACA                                                                             CCTAGAAGAG                                                                             ATGCGCCGCA                                                                             TGGGCTTGCA                                                                             TTCTGAGATT                                                                             1080                           ATCCGTGATA                                                                             CAGCTCGTAT                                                                             TGTTGGTGGA                                                                             CAGCCTTTGC                                                                             AGGGAGCAGA                                                                             AGTTCTTTCA                                                                             1140                           ACTGACCTTC                                                                             GTGCCAGTGC                                                                             AGCCTTGATT                                                                             TTGACAGGTT                                                                             TGGTAGCACA                                                                             GGGAGAAACT                                                                             1200                           GTGGTCGGTA                                                                             AATTGGTTCA                                                                             CTTGGATAGA                                                                             GGTTACTACG                                                                             GTTTCCATGA                                                                             GAAGTTGGCG                                                                             1260                           CAGCTAGGTG                                                                             CTAAGATTCA                                                                             GCGGATTGAG                                                                             GCAAATGATG                                                                             AAGATGAA        1308                           __________________________________________________________________________

In another embodiment the present invention relates to a MurA protein molecule, wherein said protein molecule comprises the sequence identified as SEQ ID NO. 2.

In a further embodiment the present invention relates to a ribonucleic acid molecule encoding MurA protein, said ribonucleic acid molecule comprising the sequence identified as SEQ ID NO. 3:

In yet another embodiment, the present invention relates to a recombinant DNA vector which incorporates the Streptococcus pneumoniae murA gene in operable linkage to gene expression sequences enabling the murA gene to be transcribed and translated in a host cell.

In still another embodiment the present invention relates to homologous or heterologous host cells which have been transformed or transfected with the cloned murA gene of Streptococcus pneumoniae such that the murA gene is expressed in the host cell.

In a still further embodiment, the present invention relates to a method for identifying compounds that inhibit the enzymatic activity of the MurA protein of Streptococcus pneumoniae.

DESCRIPTION OF THE DRAWING

FIGURE. Plasmid pPSR21, useful for high level expression of the Streptococcus pneumoniae murA gene in the heterologous procaryotic host cell Eschericia coli.

Definitions

The terms "cleavage" or "restriction" of DNA refers to the catalytic cleavage of the DNA with a restriction enzyme that acts only at certain sequences in the DNA (viz. sequence-specific endonucleases). The various restriction enzymes used herein are commercially available and their reaction conditions, cofactors, and other requirements are used in the manner well known to one of ordinary skill in the art. Appropriate buffers and substrate amounts for particular restriction enzymes are specified by the manufacturer or can readily be found in the literature.

The term "fusion protein" denotes a hybrid protein molecule not found in nature comprising a translational fusion or enzymatic fusion in which two or more different proteins or fragments thereof are covalently linked on a single polypeptide chain.

The term "plasmid" refers to an extrachromosomal genetic element. The starting plasmids herein are either commercially available, publicly available on an unrestricted basis, or can be constructed from available plasmids in accordance with published procedures. In addition, equivalent plasmids to those described are known in the art and will be apparent to the ordinarily skilled artisan.

"MurA" refers to the protein encoded by murA, UDPGlcNAc enolpyruvyl transferase.

"Recombinant DNA cloning vector" as used herein refers to any autonomously replicating agent, including, but not limited to, plasmids and phages, comprising a DNA molecule to which one or more additional DNA segments can or have been added.

The term "recombinant DNA expression vector" as used herein refers to any recombinant DNA cloning vector, for example a plasmid or phage, in which a promoter and other regulatory elements are present to enable transcription of the inserted DNA.

The term "vector" as used herein refers to a nucleic acid compound used for introducing exogenous DNA into host cells. A vector comprises a nucleotide sequence which may encode one or more protein molecules. Plasmids, cosmids, viruses, and bacteriophages, in the natural state or which have undergone recombinant engineering, are examples of commonly used vectors.

The terms "complementary" or "complementarity" as used herein refers to the capacity of purine and pyrimidine nucleotides to associate through hydrogen bonding in double stranded nucleic acid molecules. The following base pairs are complementary: guanine and cytosine; adenine and thymine; and adenine and uracil.

"Isolated nucleic acid compound" refers to any RNA or DNA sequence, however constructed or synthesized, which is locationally distinct from its natural location.

A "primer" is a nucleic acid fragment which functions as an initiating substrate for enzymatic or synthetic elongation of, for example, a nucleic acid molecule.

The term "promoter" refers to a DNA sequence which directs transcription of DNA to RNA.

A "probe" as used herein is a labeled nucleic acid compound which hybridizes with another nucleic acid compound.

The term "hybridization" as used herein refers to a process in which a single-stranded nucleic acid molecule joins with a complementary strand through nucleotide base pairing. "Selective hybridization" refers to hybridization under conditions of high stringency. The degree of hybridization depends upon, for example, the degree of complementarity, the stringency of hybridization, and the length of hybridizing strands.

The term "stringency" refers to hybridization conditions. High stringency conditions disfavor non-homologous basepairing. Low stringency conditions have the opposite effect. Stringency may be altered, for example, by temperature and salt concentration.

DETAILED DESCRIPTION

The murA gene of Streptococcus pneumoniae encodes an enzyme which catalyzes the first committed step in stem peptide biosynthesis. The stem peptide pathway is necessary for the synthesis of the peptidoglycan layer, which is part of the bacterial cell wall. There are at least 10 steps involved in stem peptide biosynthesis. The murA gene encodes UDPGlcNAc enolpyruvyl transferase (SEQ ID NO. 2), which catalyzes the transfer of the enolpyruvyl moiety of phosphoenolpyruvate (PEP) onto UDPGlcNAc.

The murA gene of Streptococcus pneumoniae comprises a DNA sequence of 1308 nucleotide base pairs (SEQ ID NO. 1). There are no intervening sequences. Those skilled in the art will recognize that owing to the degeneracy of the genetic code (i.e. 64 codons which encode 20 amino acids), numerous "silent" substitutions of nucleotide base pairs could be introduced into the sequence identified as SEQ ID NO. 1 without altering the identity of the encoded amino acid(s) or protein product. All such substitutions are intended to be within the scope of the invention.

Gene Isolation Procedures

Those skilled in the art will recogize that the murA gene may be obtained by a plurality of applicable genetic and recombinant DNA techniques including, for example, polymerase chain reaction (PCR) amplification, or de novo DNA synthesis.(See e.g., J. Sambrook et al. Molecular Cloning, 2d Ed. Chap. 14 (1989)).

Methods for constructing gene libraries in a suitable vector such as a plasmid or phage for propagation in procaryotic or eucaryotic cells are well known to those skilled in the art. See e.g. J. Sambrook et al. Supra!. Suitable cloning vectors are widely available.

Skilled artisans will recognize that the murA gene of Streptococcus pneumoniae or fragment thereof could be isolated by PCR amplification of Streptococcus pneumoniae genomic DNA or cDNA using oligonucleotide primers targeted to any suitable region of SEQ ID NO. 1. Methods for PCR amplification are widely known in the art. See e.g. PCR Protocols: A Guide to Method and Application, Ed. M. Innis et al., Academic Press (1990). The amplification reaction comprises genomic DNA, suitable enzymes, primers, and buffers, and is conveniently carried out in a DNA Thermal Cycler (Perkin Elmer Cetus, Norwalk, Conn.). A positive result is determined by detecting an appropriately-sized DNA fragment following agarose gel electrophoresis.

Protein Production Methods

One embodiment of the present invention relates to the substantially purified protein encoded by the murA gene, or functionally related proteins of Streptococcus pneumoniae.

Skilled artisans will recognize that the proteins of the present invention can be synthesized by any number of different methods. The amino acid compounds of the invention can be made by chemical methods well known in the art, including solid phase peptide synthesis or recombinant methods. Both methods are described in U.S. Pat. No. 4,617,149, incorporated herein by reference.

The principles of solid phase chemical synthesis of polypeptides are well known in the art and may be found in general texts in the area. See, e.g., H. Dugas and C. Penney, Bioorganic Chemistry (1981) Springer-Verlag, New York, 54-92. For example, peptides may be synthesized by solid-phase methodology utilizing an Applied Biosystems 430A peptide synthesizer (Applied Biosystems, Foster City, Calif.) and synthesis cycles supplied by Applied Biosystems. Protected amino acids, such as t-butoxycarbonyl-protected amino acids, and other reagents are commercially available from many chemical supply houses.

Sequential t-butoxycarbonyl chemistry using double-couple protocols are applied to the starting p-methyl benzhydryl amine resins for the production of C-terminal carboxamides. For the production of C-terminal acids, the corresponding pyridine-2-aldoxime methiodide resin is used. Asparagine, glutamine, and arginine are coupled using preformed hydroxy benzotriazole esters. Following completion of the synthesis the peptides may be deprotected and cleaved from the resin with anhydrous hydrogen fluoride containing 10% meta-cresol. Cleavage of the side chain protecting group(s) and of the peptide from the resin is carried out at zero degrees Celsius or below, preferably -20° C. for thirty minutes followed by thirty minutes at 0° C.

The protein of the present invention can also be produced by recombinant DNA methods using the cloned murA gene of Streptococcus pneumoniae. Recombinant methods are preferred if a high yield is desired. Expression of the cloned murA gene can be carried out in a variety of suitable host cells well known to those skilled in the art. The murA gene is introduced into a host cell by any suitable means, well known to those skilled in the art. While chromosomal integration of the cloned murA gene is within the scope of the present invention, it is preferred that the gene be cloned into a suitable extra-chromosomally maintained expression vector so that the coding region of the murA gene is operably linked to a constitutive or inducible promoter.

The basic steps in the recombinant production of the MurA protein are:

a) constructing a natural, synthetic or semi-synthetic DNA encoding MurA protein;

b) integrating said DNA into an expression vector in a manner suitable for expressing the MurA protein, either alone or as a fusion protein;

c) transforming or otherwise introducing said vector into an appropriate eucaryotic or prokaryotic host cell forming a recombinant host cell,

d) culturing said recombinant host cell in a manner to express the MurA protein; and

e) recovering and substantially purifying the MurA protein by any suitable means, well known to those skilled in the art.

Expressing Recombinant MurA Protein in Procaryotic and Eucaryotic Host Cells

In general, procaryotes are used for cloning DNA sequences and for constructing the vectors of the present invention. Procaryotes may also be employed in the production of the MurA protein. For example, the Escherichia coli K12 strain 294 (ATCC No. 31446) is particularly useful for the prokaryotic expression of foreign proteins. Other strains of E. coli, bacilli such as Bacillus subtilis, enterobacteriaceae such as Salmonella typhimurium or Serratia marcescans, various Pseudomonas species and other bacteria, such as Streptomyces, may also be employed as host cells in the cloning and expression of the recombinant proteins of this invention.

Promoter sequences suitable for driving the expression of genes in procaryotes include β-lactamase e.g. vector pGX2907, ATCC 39344, contains a replicon and β-lactamase gene!, lactose systems Chang et al., Nature (London), 275:615 (1978); Goeddel et al., Nature (London), 281:544 (1979)!, alkaline phosphatase, and the tryptophan (trp) promoter system vector pATH1 (ATCC 37695) which is designed to facilitate expression of an open reading frame as a trpE fusion protein under the control of the trp promoter!. Hybrid promoters such as the tac promoter (isolatable from plasmid pDR540, ATCC-37282) are also suitable. Still other bacterial promoters, whose nucleotide sequences are generally known, enable one of skill in the art to ligate such promoter sequences to DNA encoding the proteins of the instant invention using linkers or adapters to supply any required restriction sites. Promoters for use in bacterial systems also will contain a Shine-Dalgarno sequence operably linked to the DNA encoding the desired polypeptides. These examples are illustrative rather than limiting.

The protein of this invention may be synthesized either by direct expression or as a fusion protein comprising the protein of interest as a translational fusion with another protein or peptide which may be removable by enzymatic or chemical cleavage. It is often observed in the production of certain peptides in recombinant systems that expression as a fusion protein prolongs the lifespan, increases the yield of the desired peptide, or provides a convenient means of purifying the protein. A variety of peptidases (e.g. enterokinase and thrombin) which cleave a polypeptide at specific sites or digest the peptides from the amino or carboxy termini (e.g. diaminopeptidase) of the peptide chain are known. Furthermore, particular chemicals (e.g. cyanogen bromide) will cleave a polypeptide chain at specific sites. The skilled artisan will appreciate the modifications necessary to the amino acid sequence (and synthetic or semi-synthetic coding sequence if recombinant means are employed) to incorporate site-specific internal cleavage sites. See e.g., P. Carter, "Site Specific Proteolysis of Fusion Proteins", Chapter 13, in Protein Purification: From Molecular Mechanisms to Large Scale Processes, American Chemical Society, Washington, D.C. (1990).

In addition to procaryotes, a variety of mammalian cell systems and eucaryotic microorganisms such as yeast are suitable host cells. The yeast Saccharomyces cerevisiae is the most commonly used eucaryotic microorganism. A number of other yeasts such as Kluyveromyces lactis are also suitable. For expression in Saccharomyces, the plasmid YRp7 (ATCC-40053), for example, may be used. See, e.g., L. Stinchcomb, et al., Nature, 282:39 (1979); J. Kingsman et al., Gene, 7:141 (1979); S. Tschemper et al., Gene, 10:157 (1980). Plasmid YRp7 contains the TRP1 gene which provides a selectable marker for use in a trp1 auxotrophic mutant.

Purification of Recombinantly-Produced MurA Protein

An expression vector carrying the cloned murA gene of Streptococcus pneumoniae is transformed or transfected into a suitable host cell using standard methods. Cells which contain the vector are then propagated under conditions suitable for expression of the MurA protein. If the gene is under the control of an inducible promoter then suitable growth conditions would incorporate the appropriate inducer. The recombinantly-produced protein may be purified from cellular extracts of transformed cells by any suitable means.

In a preferred process for protein purification the murA gene is modified at the 5' end to incorporate several histidine residues at the amino terminus of the MurA protein product. This "histidine tag" enables a single-step protein purification method referred to as "immobilized metal ion affinity chromatography" (IMAC), essentially as described in U.S. Pat. No. 4,569,794 which hereby is incorporated by reference. The IMAC method enables rapid isolation of substantially pure MurA protein starting from a crude cellular extract.

Other embodiments of the present invention comprise isolated nucleic acid sequences which encode SEQ ID NO: 2. As skilled artisans will recognize, the amino acid compounds of the invention can be encoded by a multitude of different nucleic acid sequences because most of the amino acids are encoded by more than one codon due to the degeneracy of the genetic code. Because these alternative nucleic acid sequences would encode the same amino acid sequences, the present invention further comprises these alternate nucleic acid sequences.

The murA gene, which comprises nucleic acid encoding SEQ ID NO: 2, may be produced using synthetic methodology. The synthesis of nucleic acids is well known in the art. See, e.g., E. L. Brown, R. Belagaje, M. J. Ryan, and H. G. Khorana, Methods in Enzymology, 68:109-151 (1979). The DNA segments corresponding to the murA gene could be generated using a conventional DNA synthesizing apparatus, such as the Applied Biosystems Model 380A or 380B DNA synthesizers (Applied Biosystems, Inc., 850 Lincoln Center Drive, Foster City, Calif. 94404) which employ phosphoramidite chemistry. Alternatively, phosphotriester chemistry may be employed to synthesize the nucleic acids of this invention. See, e.g., M. J. Gait, ed., Oligonucleotide Synthesis, A Practical Approach, (1984).!

In an alternative methodology, namely PCR, the murA DNA sequence comprising a portion or all of SEQ ID NO: 1 can be generated from Streptococcus pneumoniae genomic DNA using suitable oligonucleotide primers complementary to SEQ ID NO: 1 or region therein, as described in U.S. Pat. No. 4,889,818, which hereby is incorporated by reference. Suitable protocols for performing the PCR are disclosed in, for example, PCR Protocols: A Guide to Method and Applications, Ed. Michael A. Innis et al., Academic Press, Inc. (1990).

The ribonucleic acids of the present invention may be prepared using the polynucleotide synthetic methods discussed supra, or they may be prepared enzymatically using RNA polymerase to transcribe a murA DNA template.

The most preferred systems for preparing the ribonucleic acids of the present invention employ the RNA polymerase from the bacteriophage T7 or the bacteriophage SP6. These RNA polymerases are highly specific, requiring the insertion of bacteriophage-specific sequences at the 5' end of the template to be transcribed. See, J. Sambrook, et al., supra, at 18.82-18.84.

This invention also provides nucleic acids, RNA or DNA, which are complementary to SEQ ID NO: 1 or SEQ ID NO:3.

The present invention also provides probes and primers useful for a variety of molecular biology techniques including, for example, hybridization screens of genomic or subgenomic libraries. A nucleic acid compound comprising SEQ ID NO: 1, SEQ ID NO: 3 or a complementary sequence thereof, or a fragment thereof, and which is at least 18 base pairs in length, and which will selectively hybridize to Streptococcus pneumoniae DNA or mRNA encoding murA, is provided. Preferably, the 18 or more base pair compound is DNA. A probe or primer length of at least 18 base pairs is dictated by theoretical and practical considerations. See e.g. B. Wallace and G. Miyada, "Oligonucleotide Probes for the Screening of Recombinant DNA Libraries," In Methods in Enzymology, Vol. 152, 432-442, Academic Press (1987).

These probes and primers can be prepared by enzymatic methods well known to those skilled in the art (See e.g. Sambrook et al. supra). In a most preferred embodiment these probes and primers are synthesized using chemical means as described above.

Another aspect of the present invention relates to recombinant DNA cloning vectors and expression vectors comprising the nucleic acids of the present invention. Many of the vectors encompassed within this invention are described above. The preferred nucleic acid vectors are those which comprise DNA. The most preferred recombinant DNA vectors comprise the isolated DNA sequence, SEQ ID NO: 1. Plasmid pPSR21 is an especially preferred DNA vector of the present invention.

The skilled artisan understands that choosing the most appropriate cloning vector or expression vector depends upon a number of factors including the availability of restriction enzyme sites, the type of host cell into which the vector is to be transfected or transformed, the purpose of the transfection or transformation (e.g., stable transformation as an extrachromosomal element, or integration into the host chromosome), the presence or absence of readily assayable or selectable markers (e.g., antibiotic resistance and metabolic markers of one type and another), and the number of copies of the gene to be present in the host cell.

Vectors suitable to carry the nucleic acids of the present invention comprise RNA viruses, DNA viruses, lytic bacteriophages, lysogenic bacteriophages, stable bacteriophages, plasmids, viroids, and the like. The most preferred vectors are plasmids.

When preparing an expression vector the skilled artisan understands that there are many variables to be considered, for example, whether to use a constitutive or inducible promoter. Inducible promoters are preferred because they enable high level, regulatable expression of an operably linked gene. The skilled artisan will recognize a number of inducible promoters which respond to a variety of inducers, for example, carbon source, metal ions, heat, and others. The practitioner also understands that the amount of nucleic acid or protein to be produced dictates, in part, the selection of the expression system. The addition of certain nucleotide sequences is useful for directing the localization of a recombinant protein. For example, a sequence encoding a signal peptide preceding the coding region of a gene, is useful for directing the extra-cellular export of a resulting polypeptide.

Host cells harboring the nucleic acids disclosed herein are also provided by the present invention. A preferred host is E. coli which has been transfected or transformed with a vector which comprises a nucleic acid of the present invention.

The present invention also provides a method for constructing a recombinant host cell capable of expressing SEQ ID NO: 2, said method comprising transforming or otherwise introducing into a host cell a recombinant DNA vector that comprises an isolated DNA sequence which encodes SEQ ID NO: 2. The preferred host cell is any strain of E. coli which can accomodate high level expression of an exogenously introduced gene. Preferred vectors for expression are those which comprise SEQ ID NO: 1. An especially preferred expression vector for use in E. coli is plasmid pPSR21, which comprises SEQ ID NO: 1. (See FIGURE). Transformed host cells may be cultured under conditions well known to skilled artisans such that SEQ ID NO: 2 is expressed, thereby producing MurA protein in the recombinant host cell.

For the purpose of identifying or developing inhibitors of the stem peptide pathway, it would be desirable to determine those agents which inhibit the MurA step. A method for determining whether a substance will inhibit the enzymatic reaction catalyzed by the MurA protein comprises contacting the MurA protein with a test inhibitory compound and monitoring MurA enzyme activity by any suitable means.

The instant invention provides such a screening system useful for discovering compounds which inhibit the MurA protein, said screening system comprising the steps of:

a) preparing MurA enzyme;

b) exposing said MurA enzyme to a test inhibitor;

c) introducing a specific MurA substrate; and

d) quantifying the loss of activity of said MurA enzyme.

Utilization of the screening system described above provides a means to determine compounds which interfere with stem peptide biosynthesis. This screening method may be adapted to automated procedures such as a PANDEX® (Baxter-Dade Diagnostics) system, allowing for efficient high-volume screening of potential therapeutic agents.

In such a screening protocol MurA enzyme is prepared as described herein, preferably using recombinant DNA technology. A test inhibitory compound is then introduced into the reaction vessel containing the MurA enzyme, followed by addition of enzyme substrate. Alternatively, substrate may be added simultaneously with the test compound. For example, in a preferred method radioactively or chemically-labeled substrate may be used. The products of the enzymatic reaction are assayed for the chemical label or radioactivity by any suitable means. The absence or diminution of the chemical label or radioactivity indicates the degree to which the reaction is inhibited.

Skilled artisans will recognize that IC₅₀ values are dependent on the selectivity of the compound tested. For example, a compound with an IC₅₀ which is less than 10 nM is generally considered an excellent candidate for drug therapy. However, a compound which has a lower affinity, but is selective for a particular target, may be an even better candidate. The skilled artisan will recognize that any information regarding inhibitory activity or selectivity of a particular compound is beneficial in the pharmaceutical arts.

The following examples more fully describe the present invention. Those skilled in the art will recognize that the particular reagents, equipment, and procedures described are merely illustrative and are not intended to limit the present invention in any manner.

EXAMPLE 1 Construction of a DNA Vector for Expressing Streptococcus pnuemoniae murA Gene in a Homologous or Heterologous Host

Plasmid pPSR21 (See FIGURE) is an approximately 7000 base pair expression vector suitable for expressing the murA gene of S. pneumoniae in the procaryotic host E. coli. This plasmid contains an origin of replication (Ori), an ampicillin resistance gene (Amp), useful for selecting cells which have incorporated the vector following a tranformation procedure, and further comprises the lacI gene for repression of the lac operon, as well as the T7 promoter and T7 terminator sequences in operable linkage to the coding region of the murA gene. Parent plasmid pET11A (obtained from Novogen, Madison, Wis.) was linearized by digestion with endonucleases NdeI and BamHI. Linearized pET11A was ligated to a DNA fragment bearing NdeI and BamHI sticky ends and further comprising the coding region of the S. pneumoniae murA gene.

The murA gene, which was ligated into pPSR21, was modified at the 5' end (amino terminus of encoded protein) in order to simplify purification of the encoded MurA protein product. For this purpose, an oligonucleotide encoding 8 histidine residues and a factor Xa cleavage site was inserted after the ATG start codon at nucleotide positions 1 to 3 of SEQ ID NO: 1. Placement of the histidine residues at the amino terminus of the encoded protein does not affect its activity and serves only to enable the IMAC one-step protein purification procedure (See below).

EXAMPLE 2 Expression of Streptococcus pneumoniae MurA Gene in Echerichia coli and Purification of MurA Enzyme

Plasmid pPSR21 is transformed into E. coli BL21 (DE3)(hsdS gal λcIts857 indlSam7nin5lacUV5-T7gene 1) using standard methods (See e.g. Sambrook et al. Supra). Transformants, selected for resistance to ampicillin, are chosen at random and tested for the presence of pPSR21 by agarose gel electrophoresis using quick plasmid preparations. Id. Colonies that contain pPSR21 are grown, processed, and the protein product encoded by the murA gene purified by immobilized metal ion affinity chromatography (IMAC), essentially as described in U.S. Pat. No. 4,569,794, the entire contents of which is hereby incorporated by reference.

Briefly, the IMAC column is prepared as follows. A metal-free chelating resin (e.g. SEPHAROSE 6B IDA, Pharmacia) is washed in distilled water to remove preservative substances and infused with a suitable metal ion e.g. Ni(II), Co(II), or Cu(II)! by adding a 50 mM metal chloride or metal sulfate aqueous solution until about 75% of the interstitial spaces of the resin are saturated with colored metal ion. The column is then ready to receive a crude cellular extract prepared from a recombinant host transformed or transfected with plasmid pPSR21.

After washing the column with a suitable buffer, pH 7.5 to remove unbound proteins and other materials, the bound recombinant MurA protein is eluted in a buffer at pH 4.3, essentially as described in U.S. Pat. No. 4,569,794.

EXAMPLE 3 BioChemical Assay for Inhibitors of Streptococcus pneumoniae MurA Enzyme Product

The activity of the MurA enzyme is assayed by monitoring the UDP-GlcNAc-dependent release of P_(i) from PEP. Seventy microliters of the test sample is added to 30 μl of mixture containing 10 μl of 250 mM Tris-HCl, pH 7.8, 10 μl of 100 mM UDP-GlcNAc, and 10 μl of 100 mM PEP. The reaction is incubated at 37° C. and the amount of P_(i) released at varying times is assayed by the method of Lanzetta et al. Anal. Biochem. 100, 95-97 (1979).

Inhibition studies are carried out using the reaction conditions described in the preceding paragraph. Test inhibitory compounds are added to a final concentration of between 1 mM and 10 mM, and the percentage inhibition ascertained by comparison with a control in which no test inhibitor is present.

    __________________________________________________________________________     SEQUENCE LISTING                                                               (1) GENERAL INFORMATION:                                                       (iii) NUMBER OF SEQUENCES: 3                                                   (2) INFORMATION FOR SEQ ID NO:1:                                               (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 1308 base pairs                                                    (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: DNA (genomic)                                              (iii) HYPOTHETICAL: NO                                                         (iv) ANTI-SENSE: NO                                                            (ix) FEATURE:                                                                  (A) NAME/KEY: CDS                                                              (B) LOCATION: 1..1308                                                          (xi) SEQUENCE DESCRIPTION: SEQ ID NO:1:                                        ATGAAATCAAGAGTAAAGGAAACGAGTATGGATAAAATTGTGGTTCAA48                             MetLysSerArgValLysGluThrSerMetAspLysIleValValGln                               151015                                                                         GGTGGCGATAATCGTCTGGTAGGAAGCGTGACGATCGAGGGAGCAAAA96                             GlyGlyAspAsnArgLeuValGlySerValThrIleGluGlyAlaLys                               202530                                                                         AATGCAGTCTTACCCTTGTTGGCAGCGACTATTCTAGCAAGTGAAGGA144                            AsnAlaValLeuProLeuLeuAlaAlaThrIleLeuAlaSerGluGly                               354045                                                                         AAGACCGTCTTGCAGAATGTTCCGATTTTGTCGGATGTCTTTATTATG192                            LysThrValLeuGlnAsnValProIleLeuSerAspValPheIleMet                               505560                                                                         AATCAGGTAGTTGGTGGTTTGAATGCCAAGGTTGACTTTGATGAGGAA240                            AsnGlnValValGlyGlyLeuAsnAlaLysValAspPheAspGluGlu                               65707580                                                                       GCTCATCTTGTCAAGGTGGATGCTACTGGCGACATCACTGAGGAAGCC288                            AlaHisLeuValLysValAspAlaThrGlyAspIleThrGluGluAla                               859095                                                                         CCTTACAAGTATGTCAGCAAGATGCGCGCCTCCATCGTTGTATTAGGG336                            ProTyrLysTyrValSerLysMetArgAlaSerIleValValLeuGly                               100105110                                                                      CCAATCCTTGCCCGTGTGGGTCATGCCAAGGTATCCATGCCAGGTGGT384                            ProIleLeuAlaArgValGlyHisAlaLysValSerMetProGlyGly                               115120125                                                                      TGTACGATTGGTAGCCGTCCTATTGATCTTCATTTGAAAGGTCTGGAA432                            CysThrIleGlySerArgProIleAspLeuHisLeuLysGlyLeuGlu                               130135140                                                                      GCTATGGGGGTTAAGATTAGTCAGACAGCTGGTTACATCGAAGCCAAG480                            AlaMetGlyValLysIleSerGlnThrAlaGlyTyrIleGluAlaLys                               145150155160                                                                   GCAGAACGCTTGCATGGCGCTCATATCTATATGGACTTTCCAAGTGTT528                            AlaGluArgLeuHisGlyAlaHisIleTyrMetAspPheProSerVal                               165170175                                                                      GGTGCAACGCAGAACTTGATGATGGCAGCGACTCTGGCTGATGGGGTG576                            GlyAlaThrGlnAsnLeuMetMetAlaAlaThrLeuAlaAspGlyVal                               180185190                                                                      ACAGTGATTGAGAATGCTGCGCGTGAGCCTGAGATTGTTGACTTAGCC624                            ThrValIleGluAsnAlaAlaArgGluProGluIleValAspLeuAla                               195200205                                                                      ATTCTCCTTAATGAAATGGGAGCCAAGGTCAAAGGTGCTGGTACAGAG672                            IleLeuLeuAsnGluMetGlyAlaLysValLysGlyAlaGlyThrGlu                               210215220                                                                      ACTATAACCATTACTGGTGTTGAGAAACTTCATGGTACGACTCACAAT720                            ThrIleThrIleThrGlyValGluLysLeuHisGlyThrThrHisAsn                               225230235240                                                                   GTAGTCCAAGACCGTATCGAAGCAGGAACCTTTATGGTAGCTGCTGCC768                            ValValGlnAspArgIleGluAlaGlyThrPheMetValAlaAlaAla                               245250255                                                                      ATGACTGGTGGTGATGTCTTGATTCGAGACGCTGTCTGGGAGCACAAC816                            MetThrGlyGlyAspValLeuIleArgAspAlaValTrpGluHisAsn                               260265270                                                                      CGTCCCTTGATTGCCAAGTTACTTGAAATGGGTGTTGAAGTAATTGAA864                            ArgProLeuIleAlaLysLeuLeuGluMetGlyValGluValIleGlu                               275280285                                                                      GAAGACGAAGGAATTCGTGTTCGTTCTCAACTAGAAAATCTAAAAGCT912                            GluAspGluGlyIleArgValArgSerGlnLeuGluAsnLeuLysAla                               290295300                                                                      GTTCATGTGAAAACCTTGCCCCACCCAGGATTTCCAACAGATATGCAG960                            ValHisValLysThrLeuProHisProGlyPheProThrAspMetGln                               305310315320                                                                   GCTCAATTTACAGCCTTGATGACAGTTGCAAAAGGCGAATCAACCATG1008                           AlaGlnPheThrAlaLeuMetThrValAlaLysGlyGluSerThrMet                               325330335                                                                      GTGGAGACAGTTTTCGAAAATCGTTTCCAACACCTAGAAGAGATGCGC1056                           ValGluThrValPheGluAsnArgPheGlnHisLeuGluGluMetArg                               340345350                                                                      CGCATGGGCTTGCATTCTGAGATTATCCGTGATACAGCTCGTATTGTT1104                           ArgMetGlyLeuHisSerGluIleIleArgAspThrAlaArgIleVal                               355360365                                                                      GGTGGACAGCCTTTGCAGGGAGCAGAAGTTCTTTCAACTGACCTTCGT1152                           GlyGlyGlnProLeuGlnGlyAlaGluValLeuSerThrAspLeuArg                               370375380                                                                      GCCAGTGCAGCCTTGATTTTGACAGGTTTGGTAGCACAGGGAGAAACT1200                           AlaSerAlaAlaLeuIleLeuThrGlyLeuValAlaGlnGlyGluThr                               385390395400                                                                   GTGGTCGGTAAATTGGTTCACTTGGATAGAGGTTACTACGGTTTCCAT1248                           ValValGlyLysLeuValHisLeuAspArgGlyTyrTyrGlyPheHis                               405410415                                                                      GAGAAGTTGGCGCAGCTAGGTGCTAAGATTCAGCGGATTGAGGCAAAT1296                           GluLysLeuAlaGlnLeuGlyAlaLysIleGlnArgIleGluAlaAsn                               420425430                                                                      GATGAAGATGAA1308                                                               AspGluAspGlu                                                                   435                                                                            (2) INFORMATION FOR SEQ ID NO:2:                                               (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 436 amino acids                                                    (B) TYPE: amino acid                                                           (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: protein                                                    (xi) SEQUENCE DESCRIPTION: SEQ ID NO:2:                                        MetLysSerArgValLysGluThrSerMetAspLysIleValValGln                               151015                                                                         GlyGlyAspAsnArgLeuValGlySerValThrIleGluGlyAlaLys                               202530                                                                         AsnAlaValLeuProLeuLeuAlaAlaThrIleLeuAlaSerGluGly                               354045                                                                         LysThrValLeuGlnAsnValProIleLeuSerAspValPheIleMet                               505560                                                                         AsnGlnValValGlyGlyLeuAsnAlaLysValAspPheAspGluGlu                               65707580                                                                       AlaHisLeuValLysValAspAlaThrGlyAspIleThrGluGluAla                               859095                                                                         ProTyrLysTyrValSerLysMetArgAlaSerIleValValLeuGly                               100105110                                                                      ProIleLeuAlaArgValGlyHisAlaLysValSerMetProGlyGly                               115120125                                                                      CysThrIleGlySerArgProIleAspLeuHisLeuLysGlyLeuGlu                               130135140                                                                      AlaMetGlyValLysIleSerGlnThrAlaGlyTyrIleGluAlaLys                               145150155160                                                                   AlaGluArgLeuHisGlyAlaHisIleTyrMetAspPheProSerVal                               165170175                                                                      GlyAlaThrGlnAsnLeuMetMetAlaAlaThrLeuAlaAspGlyVal                               180185190                                                                      ThrValIleGluAsnAlaAlaArgGluProGluIleValAspLeuAla                               195200205                                                                      IleLeuLeuAsnGluMetGlyAlaLysValLysGlyAlaGlyThrGlu                               210215220                                                                      ThrIleThrIleThrGlyValGluLysLeuHisGlyThrThrHisAsn                               225230235240                                                                   ValValGlnAspArgIleGluAlaGlyThrPheMetValAlaAlaAla                               245250255                                                                      MetThrGlyGlyAspValLeuIleArgAspAlaValTrpGluHisAsn                               260265270                                                                      ArgProLeuIleAlaLysLeuLeuGluMetGlyValGluValIleGlu                               275280285                                                                      GluAspGluGlyIleArgValArgSerGlnLeuGluAsnLeuLysAla                               290295300                                                                      ValHisValLysThrLeuProHisProGlyPheProThrAspMetGln                               305310315320                                                                   AlaGlnPheThrAlaLeuMetThrValAlaLysGlyGluSerThrMet                               325330335                                                                      ValGluThrValPheGluAsnArgPheGlnHisLeuGluGluMetArg                               340345350                                                                      ArgMetGlyLeuHisSerGluIleIleArgAspThrAlaArgIleVal                               355360365                                                                      GlyGlyGlnProLeuGlnGlyAlaGluValLeuSerThrAspLeuArg                               370375380                                                                      AlaSerAlaAlaLeuIleLeuThrGlyLeuValAlaGlnGlyGluThr                               385390395400                                                                   ValValGlyLysLeuValHisLeuAspArgGlyTyrTyrGlyPheHis                               405410415                                                                      GluLysLeuAlaGlnLeuGlyAlaLysIleGlnArgIleGluAlaAsn                               420425430                                                                      AspGluAspGlu                                                                   435                                                                            (2) INFORMATION FOR SEQ ID NO:3:                                               (i) SEQUENCE CHARACTERISTICS:                                                  (A) LENGTH: 1308 base pairs                                                    (B) TYPE: nucleic acid                                                         (C) STRANDEDNESS: single                                                       (D) TOPOLOGY: linear                                                           (ii) MOLECULE TYPE: mRNA                                                       (iii) HYPOTHETICAL: NO                                                         (iv) ANTI-SENSE: NO                                                            (xi) SEQUENCE DESCRIPTION: SEQ ID NO:3:                                        AUGAAAUCAAGAGUAAAGGAAACGAGUAUGGAUAAAAUUGUGGUUCAAGGUGGCGAUAAU60                 CGUCUGGUAGGAAGCGUGACGAUCGAGGGAGCAAAAAAUGCAGUCUUACCCUUGUUGGCA120                GCGACUAUUCUAGCAAGUGAAGGAAAGACCGUCUUGCAGAAUGUUCCGAUUUUGUCGGAU180                GUCUUUAUUAUGAAUCAGGUAGUUGGUGGUUUGAAUGCCAAGGUUGACUUUGAUGAGGAA240                GCUCAUCUUGUCAAGGUGGAUGCUACUGGCGACAUCACUGAGGAAGCCCCUUACAAGUAU300                GUCAGCAAGAUGCGCGCCUCCAUCGUUGUAUUAGGGCCAAUCCUUGCCCGUGUGGGUCAU360                GCCAAGGUAUCCAUGCCAGGUGGUUGUACGAUUGGUAGCCGUCCUAUUGAUCUUCAUUUG420                AAAGGUCUGGAAGCUAUGGGGGUUAAGAUUAGUCAGACAGCUGGUUACAUCGAAGCCAAG480                GCAGAACGCUUGCAUGGCGCUCAUAUCUAUAUGGACUUUCCAAGUGUUGGUGCAACGCAG540                AACUUGAUGAUGGCAGCGACUCUGGCUGAUGGGGUGACAGUGAUUGAGAAUGCUGCGCGU600                GAGCCUGAGAUUGUUGACUUAGCCAUUCUCCUUAAUGAAAUGGGAGCCAAGGUCAAAGGU660                GCUGGUACAGAGACUAUAACCAUUACUGGUGUUGAGAAACUUCAUGGUACGACUCACAAU720                GUAGUCCAAGACCGUAUCGAAGCAGGAACCUUUAUGGUAGCUGCUGCCAUGACUGGUGGU780                GAUGUCUUGAUUCGAGACGCUGUCUGGGAGCACAACCGUCCCUUGAUUGCCAAGUUACUU840                GAAAUGGGUGUUGAAGUAAUUGAAGAAGACGAAGGAAUUCGUGUUCGUUCUCAACUAGAA900                AAUCUAAAAGCUGUUCAUGUGAAAACCUUGCCCCACCCAGGAUUUCCAACAGAUAUGCAG960                GCUCAAUUUACAGCCUUGAUGACAGUUGCAAAAGGCGAAUCAACCAUGGUGGAGACAGUU1020               UUCGAAAAUCGUUUCCAACACCUAGAAGAGAUGCGCCGCAUGGGCUUGCAUUCUGAGAUU1080               AUCCGUGAUACAGCUCGUAUUGUUGGUGGACAGCCUUUGCAGGGAGCAGAAGUUCUUUCA1140               ACUGACCUUCGUGCCAGUGCAGCCUUGAUUUUGACAGGUUUGGUAGCACAGGGAGAAACU1200               GUGGUCGGUAAAUUGGUUCACUUGGAUAGAGGUUACUACGGUUUCCAUGAGAAGUUGGCG1260               CAGCUAGGUGCUAAGAUUCAGCGGAUUGAGGCAAAUGAUGAAGAUGAA1308                           __________________________________________________________________________ 

We claim:
 1. A substantially pure MurA protein from Streptococcus pneumoniae having the amino acid sequence which is SEQ ID NO:
 2. 2. A method for identifying inhibitory compounds of Streptococcus pneumoniae MurA protein activity, comprising the steps of:a) admixing in a suitable reaction bufferi) a substantially pure MurA protein as claimed in claim 1; ii) a suitable substrate; iii) a test inhibitory compound; b) measuring by any suitable means an amount of product formed; and c) comparing the amount of product formed at step (b) with a control reaction, said control reaction comprising steps (a)(i), (a)(ii), and (b) and wherein said control reaction lacks said test inhibitory compound.
 3. A method, as in claim 2 wherein the substrate of step (a)(ii) comprises UDP-GlcNAc and PEP.
 4. A method, as in claim 2 wherein the amount of product formed at step (b) is determined by measuring the amount of inorganic phosphate released.
 5. A kit useful for identifying inhibitors of stem peptide biosynthesis said kit comprising:a) a substantially pure MurA protein, as claimed in claim 1; and b) a suitable substrate for said protein. 